High-affinity ligands of the colchicine domain in tubulin based on a structure-guided design (original) (raw)
Related papers
Variations in the colchicine-binding domain provide insight into the structural switch of tubulin
Proceedings of The National Academy of Sciences, 2009
Structural changes occur in the ␣-tubulin heterodimer during the microtubule assembly/disassembly cycle. Their most prominent feature is a transition from a straight, microtubular structure to a curved structure. There is a broad range of small molecule compounds that disturbs the microtubule cycle, a class of which targets the colchicine-binding site and prevents microtubule assembly. This class includes compounds with very different chemical structures, and it is presently unknown whether they prevent tubulin polymerization by the same mechanism. To address this issue, we have determined the structures of tubulin complexed with a set of such ligands and show that they interfere with several of the movements of tubulin subunits structural elements upon its transition from curved to straight. We also determined the structure of tubulin unliganded at the colchicine site; this reveals that a -tubulin loop (termed T7) flips into this site. As with colchicine site ligands, this prevents a helix which is at the interface with ␣-tubulin from stacking onto a -tubulin  sheet as in straight protofilaments. Whereas in the presence of these ligands the interference with microtubule assembly gets frozen, by flipping in and out the -subunit T7 loop participates in a reversible way in the resistance to straightening that opposes microtubule assembly. Our results suggest that it thereby contributes to microtubule dynamic instability.
2018
Theoretical investigation of the interaction between the modifications at the C-5, C-6, and C-7 positions of the B-ring of colchicine and tubulin heterodimer has been investigated by using the molecular docking simulation. The docking results provide the energetic and structural information in terms of the binding energy, binding affinity, hydrogen bonding, and conformations of docked ligand poses with residues within colchicine binding site. Overall results show that the modified C-5 (in Model A ) and C-7 (in Model C ) of B-ring analogues give the highest binding affinities to tubulin, whereas all lowest-affinity isomers belong to the C-6 substituents (in Model B ). As expected, the docked ligands of the C-5, C-6, and C-7 of B-ring analogues which are located at the a/b intradimer interface of tubulin were shifting toward the a-subunit binding space to form drug-tubulin complexes. Keywords : colchicine, B-ring analogues, tubulin, binding affinity, molecular docking